Man pages for SQMtools
Analyze Results Generated by the 'SqueezeMeta' Pipeline
| CheckMProkaryote | CheckM reference markers for Prokaryotes |
| combineSQM | Combine several SQM objects |
| combineSQMlite | Combine several SQM or SQMlite objects |
| create_bin | Create a bin from a vector of contigs |
| exportBins | Export the bins of a SQM object |
| exportContigs | Export the contigs of a SQM object |
| exportKrona | Export the taxonomy of a SQM object into a Krona Chart |
| exportORFs | Export the ORFs of a SQM object |
| exportPathway | Export the functions of a SQM object into KEGG pathway maps |
| exportTable | Export results in tabular format |
| find_redundant_contigs | Find redundant contigs within a bin |
| Hadza | Hadza hunter-gatherer gut metagenomes |
| loadSQM | Load a SqueezeMeta project into R |
| loadSQMlite | Load tables generated by 'sqm2tables.py',... |
| MGKOs | Single Copy Phylogenetic Marker Genes from Sunagawa's group... |
| MGOGs | Single Copy Phylogenetic Marker Genes from Sunagawa's group... |
| mostAbundant | Get the N most abundant rows (or columns) from a numeric... |
| mostVariable | Get the N most variable rows (or columns) from a numeric... |
| plotBars | Plot a barplot using ggplot2 |
| plotBins | Barplot of the most abundant bins in a SQM object |
| plotFunctions | Heatmap of the most abundant functions in a SQM object |
| plotHeatmap | Plot a heatmap using ggplot2 |
| plotTaxonomy | Barplot of the most abundant taxa in a SQM object |
| RecA | RecA/RadA recombinase |
| remove_contigs_from_bin | Remove contigs from a given bin |
| rowMaxs | Return a vector with the row-wise maxima of a matrix or... |
| rowMins | Return a vector with the row-wise minima of a matrix or... |
| seqvec2fasta | Print a named vector of sequences as a fasta-formatted string |
| subsetBins | Create a SQM object containing only the requested bins, and... |
| subsetContigs | Select contigs |
| subsetFun | Filter results by function |
| subsetORFs | Select ORFs |
| subsetRand | Select random ORFs |
| subsetSamples | Filter results by sample |
| subsetTax | Filter results by taxonomy |
| summary.SQM | summary method for class SQM |
| summary.SQMbunch | summary method for class SQMbunch |
| summary.SQMlite | summary method for class SQMlite |
| USiCGs | Universal Single-Copy Genes |
